Prediction models of persistent taxane-induced peripheral neuropathy among breast cancer survivors using whole-exome sequencing

Persistent taxane-induced peripheral neuropathy (TIPN) is highly prevalent among early-stage breast cancer survivors (ESBCS) and has detrimental effect on quality of life. We leveraged logistic regression models to develop and validate polygenic prediction models to estimate the risk of persistent PN symptoms in a training cohort and validation cohort taking clinical risk factors into account. Based on 337 whole-exome sequenced ESBCS two of five prediction models for individual PN symptoms obtained AUC results above 60% when validated. Using the model for numbness in feet (35 SNVs) in the test cohort, 73% survivors were correctly predicted. For tingling in feet (55 SNVs) 70% were correctly predicted. Both models included SNVs from the ADAMTS20, APT6V0A2, CCDC88C, CYP2C8, EPHA5, NR1H3, PSKH2/APTV0D2, and SCN10A genes. For cramps in feet, difficulty climbing stairs and difficulty opening a jar the validation was unsuccessful. Polygenic prediction models including clinical risk factors can estimate the risk of persistent taxane-induced numbness in feet and tingling in feet in ESBCS.

Enhancer mutations modulate the severity of chemotherapy-induced myelosuppression

Non-small cell lung cancer is often diagnosed at advanced stages, and many patients are still treated with classical chemotherapy. The unselective nature of chemotherapy often results in severe myelosuppression. Previous studies showed that protein-coding mutations could not fully explain the predisposition to myelosuppression. Here, we investigate the possible role of enhancer mutations in myelosuppression susceptibility. We produced transcriptome and promoter-interaction maps (using HiCap) of three blood stem-like cell lines treated with carboplatin or gemcitabine. Taking advantage of publicly available enhancer datasets, we validated HiCap results in silico and in living cells using epigenetic CRISPR technology. We also developed a network approach for interactome analysis and detection of differentially interacting genes. Differential interaction analysis provided additional information on relevant genes and pathways for myelosuppression compared with differential gene expression analysis at the bulk level. Moreover, we showed that enhancers of differentially interacting genes are highly enriched for variants associated with differing levels of myelosuppression. Altogether, our work represents a prominent example of integrative transcriptome and gene regulatory datasets analysis for the functional annotation of noncoding mutations.

IFNγ directly counteracts imatinib-induced apoptosis of primary human CD34+ CML stem/progenitor cells potentially through the upregulation of multiple key survival factors

Tyrosine kinase inhibitors (TKIs) have dramatically improved the survival in chronic myeloid leukemia (CML), but residual disease typically persists even after prolonged treatment. Several lines of evidence suggest that TKIs administered to CML patients upregulate interferon γ (IFNγ) production, which may counteract the anti-tumorigenic effects of the therapy. We now show that activated T cell-conditioned medium (TCM) enhanced proliferation and counteracted imatinib-induced apoptosis of CML cells, and addition of a neutralizing anti-IFNγ antibody at least partially inhibited the anti-apoptotic effect. Likewise, recombinant IFNγ also reduced imatinib-induced apoptosis of CML cells. This anti-apoptotic effect of IFNγ was independent of alternative IFNγ signaling pathways, but could be notably diminished by STAT1-knockdown. Furthermore, IFNγ upregulated the expression of several anti-apoptotic proteins, including MCL1, PARP9, and PARP14, both in untreated and imatinib-treated primary human CD34+ CML stem/progenitor cells. Our results suggest that activated T cells in imatinib-treated CML patients can directly rescue CML cells from imatinib-induced apoptosis at least partially through the secretion of IFNγ, which exerts a rapid, STAT1-dependent anti-apoptotic effect potentially through the simultaneous upregulation of several key hematopoietic survival factors. These mechanisms may have a major clinical impact, when targeting residual leukemic stem/progenitor cells in CML.

Early changes in gene expression profiles in AML patients during induction chemotherapy

Background

Elucidation of the genetic mechanisms underlying treatment response to standard induction chemotherapy in AML patients is warranted, in order to aid in risk-adapted treatment decisions as novel treatments are emerging. In this pilot study, we explored the treatment-induced expression patterns in a small cohort of AML patients by analyzing differential gene expression (DGE) over the first 2 days of induction chemotherapy.

Methods

Blood samples were collected from ten AML patients at baseline (before treatment initiation) and during the first 2 days of treatment (Day 1; approximately 24 h, and Day 2; approximately 48 h after treatment initiation, respectively) and RNA was extracted for subsequent RNA sequencing. DGE between time points were assessed by pairwise analysis using the R package edgeR version 3.18.1 in all patients as well as in relation to treatment response (complete remission, CR, vs non-complete remission, nCR). Ingenuity Pathway Analysis (Qiagen) software was used for pathway analysis and visualization.

Results

After initial data quality control, two patients were excluded from further analysis, resulting in a final cohort of eight patients with data from all three timepoints. DGE analysis demonstrated activation of pathways with genes directly or indirectly associated with NF-κB signaling. Significant activation of the NF-κB pathway was seen in 50% of the patients 2 days after treatment start, while iNOS pathway effects could be identified already after 1 day. nCR patients displayed activation of pathways associated with cell cycle progression, oncogenesis and anti-apoptotic behavior, including the STAT3 pathway and Salvage pathways of pyrimidine ribonucleotides. Notably, a significant induction of cytidine deaminase, an enzyme responsible for the deamination of Ara-C, could be observed between baseline and Day 2 in the nCR patients but not in patients achieving CR.

Conclusions

In conclusion, we show that time-course analysis of gene expression represents a feasible approach to identify relevant pathways affected by standard induction chemotherapy in AML patients. This poses as a potential method for elucidating new drug targets and biomarkers for categorizing disease aggressiveness and evaluating treatment response. However, more studies on larger cohorts are warranted to elucidate the transcriptional basis for drug response.

The association of four genetic variants with myelosuppression in gemcitabine-treated Japanese is not evident in gemcitabine/carboplatin-treated Swedes

Gemcitabine/carboplatin‐induced myelosuppressive adverse drug reactions (ADRs) are clinical problems leading to patient suffering and dose alterations. There is a need for personalised medicine to improve treatment effects and patients' well‐being. We tested four genetic variants, rs11141915, rs1901440, rs12046844 and rs11719165, previously suggested as potential biomarkers for gemcitabine‐induced leukopenia/neutropenia in Japanese patients, in 213 Swedish gemcitabine/carboplatin‐treated non‐small cell lung cancer (NSCLC) patients. DNA was genotyped using TaqMan probes and real‐time PCR. The relationships between the risk alleles and low toxicity (non‐ADR: Common Terminology Criteria for Adverse Events [CTCAE] grades 0) or high toxicity (ADR: CTCAE grades 3–4) of platelets, leukocytes and neutrophils were evaluated using Fisher's exact test. The risk alleles did not correlate with myelosuppression, and the strongest borderline significance (not withstanding adjustment for multiple testing) was for rs1901440 (neutropenia, p = 0.043) and rs11719165 (leukopenia, p = 0.049) where the risk alleles trended towards lower toxicity, contrasting with previous study findings. Risk alleles and higher risk scores were more common among our patients. We conclude that the genetic variants do not apply to Swedish patients treated with gemcitabine/carboplatin. However, they can still be important in other populations and cohorts, especially in a gemcitabine monotherapy setting, where the causal genetic variation might influence myelosuppressive ADRs.

Activation of the μ-opioid receptor by alicyclic fentanyls: Changes from high potency full agonists to low potency partial agonists with increasing alicyclic substructure

Fentanyl analogs represent an important group of new psychoactive substances and knowing their efficacy and potency might assist in interpreting observed concentrations. The potency of fentanyl analogs can be estimated from in vitro studies and can be used to establish structure–activity relationships. In this study, recombinant CHO‐K1 cells (AequoScreen) expressing the human μ‐opioid receptor were used to establish dose–response curves via luminescent analysis for cyclopropyl‐, cyclobutyl‐, cyclopentyl‐, cyclohexyl‐, and 2,2,3,3‐tetramethylcyclopropylfentanyl (TMCPF), on three separate occasions, using eight different concentrations in an eight‐fold serial dilution in triplicates starting at ~60 μM. Fentanyl was used as a full agonist reference while morphine and buprenorphine were included for comparison. Cyclopropylfentanyl (EC₅₀ = 4.3 nM), cyclobutylfentanyl (EC50 = 6.2 nM), and cyclopentylfentanyl (EC₅₀ = 13 nM) were full agonists slightly less potent than fentanyl (EC₅₀ = 1.7 nM). Cyclohexylfentanyl (EC₅₀ = 3.1 μM, efficacy 48%) and TMCPF (EC₅₀ = 1.5 μM, efficacy 65%) were partial agonists less potent than morphine (EC₅₀ = 430 nM). Based on the results, cyclopropyl‐, cyclobutyl‐, and cyclopentylfentanyl would be expected to induce intoxication or cause fatal poisonings at similar concentrations to fentanyl, while the toxic or fatal concentrations of cyclohexylfentanyl and TMCPF would be expected to be much higher.

Genetic association of gemcitabine/carboplatin-induced leukopenia and neutropenia in non-small cell lung cancer patients using whole-exome sequencing

OBJECTIVES

Gemcitabine/carboplatin treatment is known to cause severe adverse drug reactions which can lead to the need for reduction or cessation of chemotherapy. It would be beneficial to identify patients at risk of severe hematological toxicity in advance before treatment start. This study aims to identify genetic markers for gemcitabine/carboplatin-induced leukopenia and neutropenia in non-small cell lung cancer patients.

MATERIAL AND METHODS

Whole-exome sequencing was performed on 215 patients. Association analysis was performed on single-nucleotide variants (SNVs) and genes, and the validation was based on an independent genome-wide association study (GWAS). Based on the association and validation analyses the genetic variants were then selected for and used in weighted genetic risk score (wGRS) prediction models for leukopenia and neutropenia.

RESULTS

Association analysis identified 50 and 111 SNVs, and 12 and 20 genes, for leukopenia and neutropenia, respectively. Of these SNVS 20 and 19 were partially validated for leukopenia and neutropenia, respectively. The genes SVIL (p = 2.48E-06) and EFCAB2 (p = 4.63E-06) were significantly associated with leukopenia contain the partially validated SNVs rs3740003, rs10160013, rs1547169, rs10927386 and rs10927387. The wGRS prediction models showed significantly different risk scores for high and low toxicity patients.

CONCLUSION

We have identified and partially validated genetic biomarkers in SNVs and genes correlated to gemcitabine/carboplatin-induced leukopenia and neutropenia and created wGRS models for predicting the risk of chemotherapy-induced hematological toxicity. These results provide a strong foundation for further studies of chemotherapy-induced toxicity.

ABCB1 Variation Affects Myelosuppression, Progression-free Survival and Overall Survival in Paclitaxel/Carboplatin-treated Ovarian Cancer Patients

The standard chemotherapy for ovarian cancer is paclitaxel/carboplatin. Patients often exhibit myelosuppressive toxicity, and the treatment response varies considerably. In this study, we investigated the previously reported SNPs 1199G>A (rs2229109), 1236C>T (rs1128503), 2677G>T/A (rs2032582), 3435C>T (rs1045642) in ABCB1, and 1196A>G (rs10509681) in CYP2C8 and their association with treatment-induced myelosuppression, progression-free survival (PFS) and overall survival (OS). From the phase III study, OAS-07OVA, 525 patients (All) treated with carboplatin and paclitaxel administered as Paclical (Arm A, n = 260) or Taxol^® (Arm B, n = 265) were included and genotyped using pyrosequencing. Genotype associations with myelosuppression, PFS and OS were investigated using anova, Kaplan-Meier analysis and Cox proportional hazard models. The most prominent finding was for the ABCB1 variant 3435TT, which was significantly associated with increased PFS in All (hazard ratio (HR) = 0.623), in Arm A (HR = 0.590) and in Arm B (HR = 0.627), as well as increased OS in All (HR = 0.443) and in Arm A (HR = 0.372) compared to the wild-type, 3435CC. For toxicity, the most interesting finding concerned the haplotype, including 1236TT, 2677TT and 3435TT, which was associated with higher neutrophil values in Arm B (p = 0.039) and less neutrophil decrease in All (p = 0.048) and in Arm B (p = 0.021). It is noteworthy that the results varied depending on the treatment arm which indicates that the effects of ABCB1 variants vary with the treatment regimen. Our results reflect the contradictory results of previous studies, confirming that small variations in the composition of treatment regimens and patient populations may influence the interpretation of SNPs effects on treatment outcome.

Abstract 5026: Association to drug-induced leukopenia using whole-exome sequencing of non-small cell lung cancer patients on gemcitabine/carboplatin regimen

A classical non-small cell lung cancer (NSCLC) chemotherapy treatment is gemcitabine in combination with carboplatin. The treatment is known to cause severe hematological toxicity such as leukopenia, which can lead to chemotherapy cessation or even death. It would therefore a priori be of advantage to identify patients at risk of severe leukopenia to allow for a personalized treatment approach. In this study we aim to identify genetic markers for chemotherapy induced leukopenia in non-small cell lung cancer.

In total, 212 non-small cell lung cancer patients treated with gemcitabine and carboplatin regimen were included in the study. Whole blood extracted DNA was prepared with Nextera Rapid Capture kit and whole exome sequenced using Illumina HiSeq 2500. Leukopenia was assessed from leukocyte particle count at baseline and the first cycle nadir values.

The statistical approach was to study association of single common variants (MAF > 0.01) to leukopenia using linear regression in PLINK and association of genes (common and rare variants) to leukopenia using SKATO in the R-package SKAT. An enrichment analysis, with input from the association results (p < 0.001), was performed using the online tool ConsensusPathDB-human to identify overrepresented pathways. A prediction model was created from the single variant analysis results (n=10 causal and n=10 protective) using weighted genetic risk score from the R-package PredictABEL.

The single variant analysis of common variants identified 133 variants (p < 0.001) and the gene based analysis identified 54 genes (p < 0.001). The pathway analysis identified 20 enriched pathways (p < 0.05). A prediction model was created to assess the risk of leukopenia.

The top pathway, HIF-1-alpha transcription factor network, overlaps with four genes (HDAC7, NDRG1, HK2 and CP). It can be of interest to leukopenia as regulation of HIF-1 alpha is essential for maintenance of hematopoietic stem cells in the bone marrow hypoxic niche. It has also been shown that HIF-1 alpha knocked mice are more sensitive to myelosuppressive treatment compared to unknocked mice, supporting the involvement of the pathway in chemotherapy induced myelosuppression.

We have identified variants located in genes and pathways likely to be involved in leukocyte sensitivity after exposure of gemcitabine and carboplatin. A prediction model has been created to estimate the risk that patients will suffer from severe leukopenia. The biological connection of the pathway HIF-1-alpha transcription factor network to leukopenia supports the relevance of these results. Further studies on this are of interest to improve identification of patients at high risk of severe leukopenia after gemcitabine and carboplatin treatment.

Citation Format: Anna Svedberg, Benjamín Sigurgeirsson, Niclas Björn, Sailendra Pradhananga, Eva Brandén, Hirsh Koyi, Rolf Lewensohn, Luigi De Petris, Cristina Rodríguez-Antona, María Apellániz-Ruiz, Joakim Lundeberg, Henrik Gréen. Association to drug-induced leukopenia using whole-exome sequencing of non-small cell lung cancer patients on gemcitabine/carboplatin regimen [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 5026. doi:10.1158/1538-7445.AM2017-5026

Catecholamine regulation of adipocyte lipolysis after surgery

The effect of surgical trauma on the regulation of lipolysis was studied in isolated fat cells obtained before and 24 hours after elective cholecystectomy in 12 patients who were not obese and who were healthy otherwise. Surgery was accompanied by a twofold increase of the basal rate of lipolysis and by a significant 50% elevation of the lipolytic effect of catecholamines. The actions of various agents that selectively stimulate lipolysis at different early or late steps in the cyclic adenosine monophosphate system beyond the adrenoreceptors were also increased about 50% after surgery (p less than 0.01). The properties of the beta-adrenoceptors were not altered by surgery, as assessed by radioligand binding and isoprenaline sensitivity. The antilipolytic properties of catecholamines (mediated by alpha 2-adrenoreceptors) were not influenced by cholecystectomy. Lipolysis was not altered in four subjects who had no surgery and who served as control subjects 24 hours after being given the same type of postoperative nutrition as patients who underwent cholecystectomy. We concluded that moderate surgical trauma is associated with increased lipolytic activity of fat cells. This is secondary to an enhanced ability of catecholamines to stimulate lipolysis because of a modification at the most distal steps in the cyclic adenosine monophosphate system, which may involve the protein kinase/hormone sensitive lipase complex.